bd_loglik {DDD} | R Documentation |
Loglikelihood for diversity-independent diversification model
Description
This function computes loglikelihood of a diversity-independent
diversification model for a given set of branching times and parameter
values.
Usage
bd_loglik(
pars1,
pars2,
brts,
missnumspec,
methode = "odeint::runge_kutta_cash_karp54"
)
Arguments
pars1 |
Vector of parameters:
pars1[1] corresponds to
lambda0 (speciation rate)
pars1[2] corresponds to mu0 (extinction
rate)
pars1[3] corresponds to lambda1 (decline parameter in
speciation rate) or K in diversity-dependence-like models
pars1[4] corresponds to mu1 (decline parameter in extinction rate)
|
pars2 |
Vector of model settings:
pars2[1] sets the
model of time-dependence:
- pars2[1] == 0 no time dependence
- pars2[1] == 1 speciation and/or extinction rate is exponentially
declining with time
- pars2[1] == 2 stepwise decline in
speciation rate as in diversity-dependence without extinction
- pars2[1] == 3 decline in speciation rate following deterministic
logistic equation for ddmodel = 1
- pars2[1] == 4 decline in
speciation rate such that the expected number of species matches with that
of ddmodel = 1 with the same mu
pars2[2] sets the
conditioning:
- pars[2] == 0 conditioning on stem or crown age
- pars[2] == 1 conditioning on stem or crown age and
non-extinction of the phylogeny
- pars[2] == 2 conditioning on
stem or crown age and on the total number of extant taxa (including missing
species)
- pars[2] == 3 conditioning on the total number of
extant taxa (including missing species)
pars2[3] sets whether
the likelihood is for the branching times (0) or the phylogeny (1)
pars2[4] sets whether the parameters and likelihood should be
shown
on screen (1) or not (0)
pars2[5] sets whether the first data
point is stem age (1) or crown age (2)
|
brts |
A set of branching times of a phylogeny, all positive
|
missnumspec |
The number of species that are in the clade but missing
in the phylogeny
|
methode |
The method used to solve the master equation, default is
'odeint::runge_kutta_cash_karp54'.
|
Value
The loglikelihood
Author(s)
Rampal S. Etienne, Bart Haegeman & Cesar Martinez
References
- Etienne, R.S. et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
doi: 10.1098/rspb.2011.1439
- Etienne, R.S. & B. Haegeman 2012. Am. Nat.
180: E75-E89, doi: 10.1086/667574
See Also
bd_ML
Examples
bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10,
missnumspec = 0)
[Package
DDD version 5.2.2
Index]